I prefer majora's mask over OOT, but I could see where people would dislike MM. There is a lack of a cohesive "going forward" feel to the entire thing, as your progress is reset at the end of every cycle, with only a mask to show for it. This is unfortunately fairly integral to the game being fairly bleak and depressing (for a zelda game) however, so there's not much to be done about it. OOT is fairly generic, but it's not a bad generic. It's one of my favorites of the more traditional zelda games.
Basically I feel it comes down to what you want out of a game. MM is closer to being an emotional experience (I would put that into less pretentious words if I could but a virus is currently running wild on my throat so I'm a little out of it), whereas OOT is closer to being an adventurous thing.
With majora's mask there's not really much of a conclusion, it just sort've... ends. But again, that's part of the feel of the thing! All that work just to make things to how they used to be. There's no long term threat that's been oppressing them, just a moon shows up, most people don't even believe it's a significant threat, so when it magically goes away it's very easy to just imagine everyone putting it off as a fluke and going on with their lives. No big deal. That kid was just a kid, nothing special. The entire game world is just very indifferent to the player, even as far as a zelda game goes. This combined with the oppressive feel to the game can very easily make the game not "fun" to a lot of people, and that's a perfectly respectable opinion.
Majora's mask also has that open ended interpretation of the various themes in the game (notably the final boss's various forms and the skull kid and such), and I always love the hell out of that.